On cherche à étudier l’effet de trois facteurs sur le transcriptome des racines d’Arabidopsis thaliana. Le CO2, au cours des études préliminaires, s’est montré peu influent en conditions contrôles de fer et de nitrates, et accentué en cas de stress nutritionnel. Nous reprennons ces résultats avec des fonctions génériques et propres pour en faire le résumé et de jolis graphes.
On a, pour chaque gène et chaque condition, son niveau d’expression en sortie de quantification. On labelle les conditions avec le code suivant : lettre majuscule pour le niveau fort, minuscule pour le niveau faible. Le réplicat est donné après l’underscore.
# quantification file
data <- read.csv("quantifFiles/quantifGenes.csv", h = T, sep = ",")
rownames(data) <- data$Gene
genes = which(!(grepl("__", rownames(data))))
not_quant = data[which((grepl("__", rownames(data)))), ]
data = data[genes, grepl("R", colnames(data))]
getLabel("R6")[1] "cnF_3"
[1] At_AmbientCO2_LowNitrate_Fe1
48 Levels: At_AmbientCO2_HighNitrate_Fe1 ... Sl_ElevatedCO2_LowNitrate_FeStarvation3
[1] "At_AmbientCO2_LowNitrate_Fe"
keep <- rowSums(data) >= 10
data <- data[keep, ]
group <- sapply(colnames(data), getLabel, with.rep = F)
colnames(data) <- sapply(colnames(data), getLabel)
head(data) cNF_3 cNF_2 cNF_1 cnF_2 cnF_1 cnF_3 CNF_1 CnF_2 CnF_1 CnF_3 cNf_1
AT1G01010 1526 1006 1116 1275 967 1018 854 1132 1294 1364 2325
AT1G01020 416 285 289 349 364 370 226 513 502 561 461
AT1G01030 31 15 19 29 36 28 12 47 34 47 18
cnf_2 cnf_1 cNf_2 cNf_3 cnf_3 Cnf_3 CNf_1 Cnf_1 Cnf_2 CNf_3 CNf_2
AT1G01010 2113 2193 2564 2364 2074 1987 2027 1754 1697 1537 1898
AT1G01020 407 432 614 380 502 484 467 426 415 413 462
AT1G01030 40 32 44 37 27 42 39 36 40 37 37
CNF_3 CNF_2
AT1G01010 816 912
AT1G01020 223 312
AT1G01030 15 19
[ reached 'max' / getOption("max.print") -- omitted 3 rows ]
[1] 23342 24
[1] "cNF_3" "cNF_2" "cNF_1" "cnF_2" "cnF_1" "cnF_3" "CNF_1" "CnF_2" "CnF_1"
[10] "CnF_3" "cNf_1" "cnf_2" "cnf_1" "cNf_2" "cNf_3" "cnf_3" "Cnf_3" "CNf_1"
[19] "Cnf_1" "Cnf_2" "CNf_3" "CNf_2" "CNF_3" "CNF_2"
cNF_3 cNF_2 cNF_1 cnF_2 cnF_1 cnF_3 CNF_1 CnF_2
1404.4841 1137.1461 1370.4972 1234.5941 975.1056 1079.3725 1464.9136 1068.1962
CnF_1 CnF_3 cNf_1 cnf_2 cnf_1 cNf_2 cNf_3 cnf_3
1184.6501 1186.8721 2176.3477 2035.5245 1879.4058 2023.3233 2118.1681 1941.6821
Cnf_3 CNf_1 Cnf_1 Cnf_2 CNf_3 CNf_2 CNF_3 CNF_2
1766.0503 1878.6843 1666.8990 1566.9834 1652.5818 1823.3202 1342.1000 1267.1018
On définit les conditions contrôle comme suit : CO2 ambiant et fort fer.
g = list()
method = "edger"
labels <- c("cNF", "cnF")
genes1 <- dualDE(data, labels, pval = 0.01, method = method) (Intercept) groupcnF
1 1 0
2 1 0
3 1 0
4 1 1
5 1 1
6 1 1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"
[1] "cNF_3" "cNF_2" "cNF_1" "cnF_2" "cnF_1" "cnF_3"
cNF_3 cNF_2 cNF_1 cnF_2 cnF_1 cnF_3
0.9859482 0.9865531 0.9545113 1.0150637 1.0299591 1.0279646
[1] "2803 genes DE"
(Intercept) groupCnF
1 1 0
2 1 0
3 1 0
4 1 1
5 1 1
6 1 1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"
[1] "CNF_1" "CNF_3" "CNF_2" "CnF_2" "CnF_1" "CnF_3"
CNF_1 CNF_3 CNF_2 CnF_2 CnF_1 CnF_3
0.9793780 0.9377198 0.9911882 1.0424709 1.0209230 1.0283201
[1] "1811 genes DE"
(Intercept) groupcnf
1 1 0
2 1 0
3 1 0
4 1 1
5 1 1
6 1 1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"
[1] "cNf_1" "cNf_2" "cNf_3" "cnf_2" "cnf_1" "cnf_3"
cNf_1 cNf_2 cNf_3 cnf_2 cnf_1 cnf_3
0.9927341 1.0205843 0.9891514 0.9943126 1.0031887 1.0000289
[1] "5356 genes DE"
(Intercept) groupCnf
1 1 0
2 1 0
3 1 0
4 1 1
5 1 1
6 1 1
attr(,"assign")
[1] 0 1
attr(,"contrasts")
attr(,"contrasts")$group
[1] "contr.treatment"
[1] "CNf_1" "CNf_3" "CNf_2" "Cnf_3" "Cnf_1" "Cnf_2"
CNf_1 CNf_3 CNf_2 Cnf_3 Cnf_1 Cnf_2
1.0043575 1.0334462 1.0275269 0.9519021 0.9851404 0.9976269
[1] "2673 genes DE"
On visualise les gènes différentiellement exprimés en commun entre les différents niveaux des autres facteurs.
library(ggVennDiagram)
library(VennDiagram)
gene_list <- list()
for (comp in names(g)) {
print(g[[comp]])
gene_list[[comp]] <- g[[comp]]$gene_id
} gene_id a.value m.value p.value q.value rank estimatedDEG
1 AT1G29100 7.527717 -3.844547 3.578192e-138 8.352216e-134 1 1
2 AT1G19250 8.839658 -3.648727 1.878457e-127 2.192347e-123 2 1
3 AT2G13810 8.469376 -4.131913 1.462868e-124 1.138209e-120 3 1
4 AT5G33355 6.962703 -5.152094 8.806368e-116 5.138956e-112 4 1
5 AT4G21680 7.657504 -3.886983 1.141541e-114 5.329171e-111 5 1
6 AT4G26050 10.258910 -2.260091 1.152467e-95 4.483480e-92 6 1
7 AT2G41810 7.414076 -4.047054 8.398511e-92 2.800544e-88 7 1
8 AT4G22640 9.630374 -1.975045 1.839254e-80 5.366485e-77 8 1
9 AT4G25100 9.022566 -2.067878 7.469292e-71 1.937202e-67 9 1
upreg
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
[ reached 'max' / getOption("max.print") -- omitted 2794 rows ]
gene_id a.value m.value p.value q.value rank estimatedDEG
1 AT2G41810 6.909960 -4.891457 5.753358e-166 1.342949e-161 1 1
2 AT4G21680 7.158203 -3.903113 1.079396e-127 1.259763e-123 2 1
3 AT5G33355 7.532822 -3.942011 1.137090e-79 8.847318e-76 3 1
4 AT4G26050 9.901752 -2.410582 3.640522e-76 2.124427e-72 4 1
5 AT2G43890 4.534486 -4.585951 5.500546e-52 2.567875e-48 5 1
6 AT4G13420 7.045056 3.418569 6.910049e-50 2.688239e-46 6 1
7 AT4G11393 2.688467 -6.030749 5.311806e-40 1.771260e-36 7 1
8 AT3G45060 3.835388 -4.139280 1.476109e-35 4.306917e-32 8 1
9 AT1G51840 8.737173 1.711245 6.237559e-35 1.617746e-31 9 1
upreg
1 0
2 0
3 0
4 0
5 0
6 1
7 0
8 0
9 1
[ reached 'max' / getOption("max.print") -- omitted 1802 rows ]
gene_id a.value m.value p.value q.value rank estimatedDEG
1 AT1G08100 8.250556 7.543363 1.061212e-240 2.477082e-236 1 1
2 AT4G19680 7.581300 -5.390613 1.732236e-215 2.021692e-211 2 1
3 AT4G31970 10.071433 4.120985 6.675358e-196 5.193874e-192 3 1
4 AT4G13250 10.098952 3.612679 1.457726e-189 8.506561e-186 4 1
5 AT1G60050 9.440827 5.561353 2.298538e-189 1.073050e-185 5 1
6 AT4G01390 8.024264 5.780911 9.500326e-178 3.695943e-174 6 1
7 AT1G26390 9.011257 3.803360 1.268011e-153 4.228272e-150 7 1
8 AT1G60470 9.278972 3.398056 1.922528e-150 5.609457e-147 8 1
9 AT1G52070 6.816105 -6.878196 7.952279e-147 2.062468e-143 9 1
upreg
1 1
2 0
3 1
4 1
5 1
6 1
7 1
8 1
9 0
[ reached 'max' / getOption("max.print") -- omitted 5347 rows ]
gene_id a.value m.value p.value q.value rank estimatedDEG
1 AT5G37990 8.804797 4.793179 1.242358e-182 2.899912e-178 1 1
2 AT3G55970 6.219576 5.310631 9.095523e-97 1.061538e-92 2 1
3 AT2G43510 9.062836 3.025254 2.217784e-86 1.725584e-82 3 1
4 AT4G21680 11.255880 -2.409529 8.268693e-85 4.825196e-81 4 1
5 AT1G32350 7.026600 3.559752 4.914056e-73 2.294078e-69 5 1
6 AT3G45060 9.354052 -2.056677 4.116341e-69 1.601394e-65 6 1
7 AT1G26390 9.590338 2.992967 4.952257e-68 1.651365e-64 7 1
8 AT2G29460 9.917335 1.860758 3.822791e-66 1.115395e-62 8 1
9 AT1G52890 8.325089 3.151416 1.724274e-65 4.472000e-62 9 1
upreg
1 1
2 1
3 1
4 0
5 1
6 0
7 1
8 1
9 1
[ reached 'max' / getOption("max.print") -- omitted 2664 rows ]
partitions <- get.venn.partitions(gene_list, keep.elements = T)
partitions$shared <- rowSums(partitions[1:4])
partitions <- partitions[order(-partitions$shared), ]
common_genes <- unlist(partitions[1, "..values.."])
results <- getBM(filters = "ensembl_gene_id", attributes = c("ensembl_gene_id", "description",
"external_gene_name", "entrezgene_id"), values = common_genes, mart = mart)
results <- results[!rownames(results) %in% which(duplicated(results$ensembl_gene_id)),
]
kable(results)| ensembl_gene_id | description | external_gene_name | entrezgene_id |
|---|---|---|---|
| AT1G01560 | Mitogen-activated protein kinase 11 [Source:UniProtKB/Swiss-Prot;Acc:Q9LMM5] | MPK11 | 839523 |
| AT1G01580 | ferric reduction oxidase 2 [Source:TAIR;Acc:AT1G01580] | FRO2 | 839411 |
| AT1G02920 | Glutathione S-transferase F7 [Source:UniProtKB/Swiss-Prot;Acc:Q9SRY5] | GSTF7 | 839295 |
| AT1G02930 | Glutathione S-transferase F6 [Source:UniProtKB/Swiss-Prot;Acc:P42760] | GSTF6 | 839515 |
| AT1G05010 | 1-aminocyclopropane-1-carboxylate oxidase 4 [Source:UniProtKB/Swiss-Prot;Acc:Q06588] | ACO4 | 839345 |
| AT1G08050 | T6D22.13 [Source:UniProtKB/TrEMBL;Acc:Q9LN03] | 837321 | |
| AT1G10550 | Probable xyloglucan endotransglucosylase/hydrolase protein 33 [Source:UniProtKB/Swiss-Prot;Acc:Q8LC45] | XTH33 | 837596 |
| AT1G13490 | F13B4.1 protein [Source:UniProtKB/TrEMBL;Acc:Q9FZ74] | 837909 | |
| AT1G14260 | At1g14260 [Source:UniProtKB/TrEMBL;Acc:Q4PS45] | 837987 | |
| AT1G14520 | myo-inositol oxygenase 1 [Source:TAIR;Acc:AT1G14520] | MIOX1 | 838014 |
| AT1G14880 | Protein PLANT CADMIUM RESISTANCE 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9LQU2] | PCR1 | 838053 |
| AT1G15010 | Mediator of RNA polymerase II transcription subunit [Source:UniProtKB/TrEMBL;Acc:Q8LCU9] | 838066 | |
| AT1G16160 | WAKL5 [Source:UniProtKB/TrEMBL;Acc:A0A178W9G0] | WAKL5 | 838185 |
| AT1G16670 | Cold-responsive protein kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q93YN1] | CRPK1 | 838236 |
| AT1G18970 | Germin-like protein subfamily T member 1 [Source:UniProtKB/Swiss-Prot;Acc:P92995] | GLP1 | 838478 |
| AT1G19020 | CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase [Source:UniProtKB/TrEMBL;Acc:Q8VYY6] | 838483 | |
| AT1G19250 | Probable flavin-containing monooxygenase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9LMA1] | FMO1 | 838508 |
| AT1G20190 | Expansin-A11 [Source:UniProtKB/Swiss-Prot;Acc:Q9LNU3] | EXPA11 | 838608 |
| AT1G21110 | Indole glucosinolate O-methyltransferase 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9LPU6] | IGMT3 | 838707 |
| AT1G21120 | O-methyltransferase family protein [Source:TAIR;Acc:AT1G21120] | 838708 | |
| AT1G21130 | Indole glucosinolate O-methyltransferase 4 [Source:UniProtKB/Swiss-Prot;Acc:Q9LPU8] | IGMT4 | 838709 |
| AT1G24620 | Probable calcium-binding protein CML25 [Source:UniProtKB/Swiss-Prot;Acc:Q9FYK2] | CML25 | 839076 |
| AT1G26380 | Berberine bridge enzyme-like 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9FZC4] | FOX1 | 839180 |
| AT1G26390 | Berberine bridge enzyme-like 4 [Source:UniProtKB/Swiss-Prot;Acc:Q9FZC5] | FOX2 | 839181 |
| AT1G26420 | Berberine bridge enzyme-like 7 [Source:UniProtKB/Swiss-Prot;Acc:Q9FZC8] | FOX5 | 839184 |
| AT1G27730 | Zinc finger protein ZAT10 [Source:UniProtKB/Swiss-Prot;Acc:Q96289] | ZAT10 | 839666 |
| AT1G28370 | ERF domain protein 11 [Source:TAIR;Acc:AT1G28370] | ERF11 | 839733 |
| AT1G29025 | Calcium-binding EF-hand family protein [Source:UniProtKB/TrEMBL;Acc:F4HZU9] | 10723075 | |
| AT1G29640 | At1g29640 [Source:UniProtKB/TrEMBL;Acc:Q9C7N7] | 839841 | |
| AT1G30560 | G3Pp3 [Source:UniProtKB/TrEMBL;Acc:A0A178WI18] | 839936 | |
| AT1G30700 | Berberine bridge enzyme-like 8 [Source:UniProtKB/Swiss-Prot;Acc:Q9SA85] | 839950 | |
| AT1G33890 | Immune-associated nucleotide-binding protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9C8U6] | IAN3 | 840286 |
| AT1G45145 | Thioredoxin H5 [Source:UniProtKB/Swiss-Prot;Acc:Q39241] | TRX5 | 841082 |
| AT1G47395 | At1g47390 [Source:UniProtKB/TrEMBL;Acc:Q8GUL3] | 841143 | |
| AT1G47400 | unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G47395.1); Ha. [Source:TAIR;Acc:AT1G47400] | 841144 | |
| AT1G47560 | Exocyst complex component SEC3B [Source:UniProtKB/Swiss-Prot;Acc:Q9SX86] | SEC3B | 841165 |
| AT1G49000 | At1g49000 [Source:UniProtKB/TrEMBL;Acc:Q9M9A2] | 841322 | |
| AT1G49240 | Actin-8 [Source:UniProtKB/Swiss-Prot;Acc:Q96293] | ACT8 | 841347 |
| AT1G50060 | CAP (Cysteine-rich secretory proteins, Antigen 5, and Pathogenesis-related 1 protein) superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q9LPM7] | 841430 | |
| AT1G53625 | At1g53625 [Source:UniProtKB/TrEMBL;Acc:Q9LPH9] | 841798 | |
| AT1G53950 | F15I1.4 protein [Source:UniProtKB/TrEMBL;Acc:Q9SYF2] | 28717351 | |
| AT1G55110 | Protein indeterminate-domain 7 [Source:UniProtKB/Swiss-Prot;Acc:Q8H1F5] | IDD7 | 841954 |
| AT1G56430 | Probable nicotianamine synthase 4 [Source:UniProtKB/Swiss-Prot;Acc:Q9C7X5] | NAS4 | 842096 |
| AT1G57630 | Disease resistance protein RPP1-WsB, putative [Source:UniProtKB/TrEMBL;Acc:Q9FVT9] | 842139 | |
| AT1G57990 | PUP18 [Source:UniProtKB/TrEMBL;Acc:A0A178WC51] | PUP18 | 842166 |
| AT1G58300 | Heme oxygenase 4, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:Q9LQC0] | HO4 | 842199 |
| AT1G58320 | Protein PLANT CADMIUM RESISTANCE 9 [Source:UniProtKB/Swiss-Prot;Acc:P0CW98] | PCR9 | 842201 |
| AT1G60750 | Probable aldo-keto reductase 6 [Source:UniProtKB/Swiss-Prot;Acc:F4HPY8] | 3767587 | |
| AT1G61080 | Hydroxyproline-rich glycoprotein family protein [Source:TAIR;Acc:AT1G61080] | 842400 | |
| AT1G62280 | SLAH1 [Source:UniProtKB/TrEMBL;Acc:A0A178W8P4] | SLAH1 | 842525 |
| AT1G62660 | Acid beta-fructofuranosidase 3, vacuolar [Source:UniProtKB/Swiss-Prot;Acc:Q43348] | BFRUCT3 | 842563 |
| AT1G63550 | Cysteine-rich repeat secretory protein 9 [Source:UniProtKB/Swiss-Prot;Acc:Q5Q0E2] | CRRSP9 | 842660 |
| AT1G64370 | Filaggrin-like protein [Source:UniProtKB/TrEMBL;Acc:Q9C7W1] | 842744 | |
| AT1G65486 | unknown protein; FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: endomembrane system; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT1G65490.1); Ha. [Source:TAIR;Acc:AT1G65486] | 6240283 | |
| AT1G65845 | At1g65844 [Source:UniProtKB/TrEMBL;Acc:Q9SHX3] | 842895 | |
| AT1G66780 | Protein DETOXIFICATION [Source:UniProtKB/TrEMBL;Acc:A0A178W985] | DTX8 | 842996 |
| AT1G67000 | LEAF RUST 10 DISEASE-RESISTANCE LOCUS RECEPTOR-LIKE PROTEIN KINASE-like 2.8 [Source:UniProtKB/Swiss-Prot;Acc:Q3ECH2] | LRK10L-2.8 | 843018 |
| AT1G70110 | Putative L-type lectin-domain containing receptor kinase V.1 [Source:UniProtKB/Swiss-Prot;Acc:O04534] | LECRK51 | 843347 |
| AT1G70170 | Metalloendoproteinase 2-MMP [Source:UniProtKB/Swiss-Prot;Acc:O04529] | 2MMP | 843353 |
| AT1G70260 | WAT1-related protein At1g70260 [Source:UniProtKB/Swiss-Prot;Acc:F4I5D5] | 843362 | |
| AT1G70690 | PDLP5 [Source:UniProtKB/TrEMBL;Acc:A0A178WPB2] | CRRSP2 | 843406 |
| AT1G72430 | Auxin-responsive protein SAUR78 [Source:UniProtKB/Swiss-Prot;Acc:Q9C9E1] | SAUR78 | 843575 |
| AT1G73500 | Mitogen-activated protein kinase kinase 9 [Source:UniProtKB/Swiss-Prot;Acc:Q9FX43] | MKK9 | 843685 |
| AT1G74710 | ADC synthase superfamily protein [Source:TAIR;Acc:AT1G74710] | EDS16 | 843810 |
| AT1G75750 | GASA1 [Source:UniProtKB/TrEMBL;Acc:A0A178W4S5] | GASA1 | 843908 |
| AT1G76220 | T23E18.15 [Source:UniProtKB/TrEMBL;Acc:Q9SGR2] | 843955 | |
| AT1G76520 | Protein PIN-LIKES 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9C9K5] | PILS3 | 843985 |
| AT1G77520 | O-methyltransferase family protein [Source:UniProtKB/TrEMBL;Acc:Q9CAQ4] | 844088 | |
| AT1G80240 | At1g80240 [Source:UniProtKB/TrEMBL;Acc:Q9SSB7] | 844364 | |
| AT2G02120 | Defensin-like protein 4 [Source:UniProtKB/Swiss-Prot;Acc:Q41914] | PDF2.1 | 814743 |
| AT2G15220 | At2g15220/F15A23.4 [Source:UniProtKB/TrEMBL;Acc:Q9SKL6] | 816011 | |
| AT2G15880 | Pollen-specific leucine-rich repeat extensin-like protein 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9XIL9] | PEX3 | 816084 |
| AT2G16660 | At2g16660/T24I21.7 [Source:UniProtKB/TrEMBL;Acc:Q9SLF1] | 816167 | |
| AT2G18690 | Expressed protein [Source:UniProtKB/TrEMBL;Acc:Q9ZV49] | 816384 | |
| AT2G19060 | GDSL esterase/lipase At2g19060 [Source:UniProtKB/Swiss-Prot;Acc:O64469] | 816423 | |
| AT2G19970 | At2g19970 [Source:UniProtKB/TrEMBL;Acc:Q9SL83] | 816516 | |
| AT2G19990 | PR-1-like protein [Source:UniProtKB/TrEMBL;Acc:A0A178VRT6] | PR-1-LIKE | 816518 |
| AT2G20520 | Fasciclin-like arabinogalactan protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q9SIL7] | FLA6 | 816574 |
| AT2G22500 | Mitochondrial uncoupling protein 5 [Source:UniProtKB/Swiss-Prot;Acc:Q9SJY5] | PUMP5 | 816783 |
| AT2G23620 | Methylesterase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q8S8S9] | MES1 | 816894 |
| AT2G25460 | CONTAINS InterPro DOMAIN/s: C2 calcium-dependent membrane targeting (InterPro:IPR000008); BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT5G04860.1); Ha. [Source:TAIR;Acc:AT2G25460] | 817084 | |
| AT2G26400 | acireductone dioxygenase 3 [Source:TAIR;Acc:AT2G26400] | ARD | 817180 |
| AT2G26530 | AR781 [Source:UniProtKB/TrEMBL;Acc:A0A178VPT1] | AR781 | 817194 |
| AT2G26560 | Patatin-like protein 2 [Source:UniProtKB/Swiss-Prot;Acc:O48723] | PLP2 | 817197 |
| AT2G29480 | Glutathione S-transferase U2 [Source:UniProtKB/Swiss-Prot;Acc:Q9ZW29] | GSTU2 | 817497 |
| AT2G30550 | Phospholipase A1-Igamma2, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:Q3EBR6] | 817604 | |
| AT2G32620 | Cellulose synthase-like protein B2 [Source:UniProtKB/Swiss-Prot;Acc:O80899] | CSLB2 | 817822 |
| AT2G36110 | Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q9SIH3] | 818184 | |
| AT2G36260 | Iron-sulfur assembly protein IscA-like 3, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q8L8C0] | 818198 | |
| AT2G37780 | Cysteine/Histidine-rich C1 domain family protein [Source:UniProtKB/TrEMBL;Acc:F4IR19] | 818355 | |
| AT2G37810 | Cysteine/Histidine-rich C1 domain family protein [Source:UniProtKB/TrEMBL;Acc:Q4PSR5] | 818358 | |
| AT2G38320 | Protein trichome birefringence-like 34 [Source:UniProtKB/Swiss-Prot;Acc:O80919] | TBL34 | 818412 |
| AT2G38490 | CBL-interacting serine/threonine-protein kinase 22 [Source:UniProtKB/Swiss-Prot;Acc:O80902] | CIPK22 | 818431 |
| AT2G38500 | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q8GY13] | 818432 | |
| AT2G39200 | MLO-like protein [Source:UniProtKB/TrEMBL;Acc:A0A178VNS1] | MLO12 | 818505 |
| AT2G41240 | BHLH100 [Source:UniProtKB/TrEMBL;Acc:A0A384LFW4] | BHLH100 | 818723 |
| AT2G41380 | At2g41380 [Source:UniProtKB/TrEMBL;Acc:Q9ZVC3] | 818736 | |
| AT2G41810 | Uncharacterized protein At2g41810 [Source:UniProtKB/TrEMBL;Acc:O22939] | 818780 | |
| AT2G42850 | CYP718 [Source:UniProtKB/TrEMBL;Acc:A0A178VUF2] | CYP718 | 818885 |
| AT2G45360 | Ankyrin repeat/KH domain protein (DUF1442) [Source:UniProtKB/TrEMBL;Acc:O22136] | 819144 | |
| AT3G01420 | Alpha-dioxygenase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9SGH6] | DOX1 | 821135 |
| AT3G02850 | SKOR [Source:UniProtKB/TrEMBL;Acc:A0A178VHK5] | SKOR | 821052 |
| AT3G03500 | T21P5.8 protein [Source:UniProtKB/TrEMBL;Acc:Q9SRQ4] | 821247 | |
| AT3G05155 | Major facilitator superfamily protein [Source:TAIR;Acc:AT3G05155] | 819678 | |
| AT3G07460 | Protein of unknown function, DUF538 [Source:TAIR;Acc:AT3G07460] | 819934 | |
| AT3G07720 | AT3g07720/F17A17_6 [Source:UniProtKB/TrEMBL;Acc:Q9S7W4] | 819963 | |
| AT3G09220 | Laccase-7 [Source:UniProtKB/Swiss-Prot;Acc:Q9SR40] | LAC7 | 820078 |
| AT3G11370 | Cysteine/Histidine-rich C1 domain family protein [Source:UniProtKB/TrEMBL;Acc:Q9CAY7] | 820309 | |
| AT3G12230 | Serine carboxypeptidase-like 14 [Source:UniProtKB/Swiss-Prot;Acc:Q9C7D3] | SCPL14 | 820403 |
| AT3G12820 | Transcription factor MYB10 [Source:UniProtKB/Swiss-Prot;Acc:Q9LTV4] | AtMYB10 | 820464 |
| AT3G12900 | 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q9LE86] | 820473 | |
| AT3G13950 | AT3G13950 protein [Source:UniProtKB/TrEMBL;Acc:B9DG91] | 820608 | |
| AT3G14990 | Protein DJ-1 homolog A [Source:UniProtKB/Swiss-Prot;Acc:Q9FPF0] | DJ1A | 820728 |
| AT3G16390 | Nitrile-specifier protein 3 [Source:UniProtKB/Swiss-Prot;Acc:O04318] | NSP3 | 820886 |
| AT3G18560 | AT3g18560/K24M9_5 [Source:UniProtKB/TrEMBL;Acc:Q9LII3] | 821387 | |
| AT3G19430 | Late embryogenesis abundant protein-related / LEA protein-like protein [Source:UniProtKB/TrEMBL;Acc:A0A178VGJ3] | 821477 | |
| AT3G19580 | ZF2 [Source:UniProtKB/TrEMBL;Acc:A0A178VJ97] | AZF2 | 821495 |
| AT3G21560 | UGT84A2 [Source:UniProtKB/TrEMBL;Acc:A0A384L2P1] | UGT84A2 | 821710 |
| AT3G22120 | Cell wall-plasma membrane linker protein [Source:UniProtKB/TrEMBL;Acc:A0A1I9LSA3] | CWLP | 821775 |
| AT3G22840 | ELIP1 [Source:UniProtKB/TrEMBL;Acc:A0A178VCA8] | ELIP1 | 821855 |
| AT3G25730 | AP2/ERF and B3 domain-containing transcription factor ARF14 [Source:UniProtKB/Swiss-Prot;Acc:Q9LS06] | ARF14 | 822164 |
| AT3G28510 | AAA-ATPase At3g28510 [Source:UniProtKB/Swiss-Prot;Acc:Q9LH84] | 822481 | |
| AT3G29250 | Short-chain dehydrogenase reductase 4 [Source:UniProtKB/Swiss-Prot;Acc:F4J2Z7] | SDR4 | 822580 |
| AT3G45650 | Nitrate excretion transporter1 [Source:UniProtKB/TrEMBL;Acc:A0A1I9LSG9] | NAXT1 | 823707 |
| AT3G46340 | Putative receptor-like protein kinase At3g46340 [Source:UniProtKB/Swiss-Prot;Acc:Q9SNA3] | 823779 | |
| AT3G47420 | Putative glycerol-3-phosphate transporter 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9C5L3] | ATPS3 | 823896 |
| AT3G48520 | CYP94B3 [Source:UniProtKB/TrEMBL;Acc:A0A178V8H3] | CYP94B3 | 824011 |
| AT3G48850 | Mitochondrial phosphate carrier protein 2, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q9M2Z8] | MPT2 | 824046 |
| AT3G49845 | WIH3 [Source:UniProtKB/TrEMBL;Acc:A0A384LFL0] | 6240705 | |
| AT3G50660 | Cytochrome P450 90B1 [Source:UniProtKB/Swiss-Prot;Acc:O64989] | CYP90B1 | 824229 |
| AT3G53150 | UDP-glucosyl transferase 73D1 [Source:TAIR;Acc:AT3G53150] | UGT73D1 | NA |
| AT3G53590 | Leucine-rich repeat protein kinase family protein [Source:TAIR;Acc:AT3G53590] | NA | |
| AT3G53600 | At3g53600 [Source:UniProtKB/TrEMBL;Acc:Q9LFG0] | 824528 | |
| AT3G55470 | At3g55470 [Source:UniProtKB/TrEMBL;Acc:Q9M2T2] | 824713 | |
| AT3G55740 | Proline transporter 2 [Source:UniProtKB/Swiss-Prot;Acc:P92962] | PROT2 | 824740 |
| AT3G55790 | Transmembrane protein [Source:UniProtKB/TrEMBL;Acc:Q9M045] | 824745 | |
| AT3G56970 | Transcription factor ORG2 [Source:UniProtKB/Swiss-Prot;Acc:Q9M1K1] | ORG2 | 824864 |
| AT3G56980 | Transcription factor ORG3 [Source:UniProtKB/Swiss-Prot;Acc:Q9M1K0] | ORG3 | 824865 |
| AT3G59080 | AT3g59080/F17J16_130 [Source:UniProtKB/TrEMBL;Acc:Q9LYS8] | 825077 | |
| AT3G59350 | Protein kinase superfamily protein [Source:UniProtKB/TrEMBL;Acc:A0A1I9LM53] | 825104 | |
| AT3G59930 | Defensin-like protein 206 [Source:UniProtKB/Swiss-Prot;Acc:Q94JR6] | 825163 | |
| AT3G63380 | Calcium-transporting ATPase [Source:UniProtKB/TrEMBL;Acc:A0A178VEV7] | ACA12 | 825513 |
| AT4G00910 | Aluminium activated malate transporter family protein [Source:TAIR;Acc:AT4G00910] | 827985 | |
| AT4G01390 | TRAF-like family protein [Source:UniProtKB/TrEMBL;Acc:F4JI18] | 828075 | |
| AT4G01630 | Expansin [Source:UniProtKB/TrEMBL;Acc:A0A178UWZ2] | EXPA17 | 827983 |
| AT4G04570 | Cysteine-rich receptor-like protein kinase 40 [Source:UniProtKB/Swiss-Prot;Acc:Q9SYS3] | CRK40 | 825789 |
| AT4G08380 | Extensin-like protein [Source:UniProtKB/TrEMBL;Acc:Q9STN0] | 826395 | |
| AT4G08570 | Heavy metal-associated isoprenylated plant protein 24 [Source:UniProtKB/Swiss-Prot;Acc:O81464] | HIPP24 | 826418 |
| AT4G10500 | Protein DMR6-LIKE OXYGENASE 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9ZSA8] | DLO1 | 826642 |
| AT4G10530 | Subtilase family protein [Source:TAIR;Acc:AT4G10530] | NA | |
| AT4G10540 | Subtilisin-like protease SBT3.8 [Source:UniProtKB/Swiss-Prot;Acc:Q9SZY3] | SBT3.8 | 826646 |
| AT4G11393 | Putative defensin-like protein 202 [Source:UniProtKB/Swiss-Prot;Acc:Q2V3J6] | 3770126 | |
| AT4G12545 | Putative lipid-binding protein AIR1B [Source:UniProtKB/Swiss-Prot;Acc:Q9ZSP6] | AIR1B | 826867 |
| AT4G12550 | Putative lipid-binding protein AIR1 [Source:UniProtKB/Swiss-Prot;Acc:Q9S7I2] | AIR1 | 826868 |
| AT4G13420 | Potassium transporter [Source:UniProtKB/TrEMBL;Acc:Q53XI1] | POT5 | 826973 |
| AT4G14280 | ARM repeat superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q1PE83] | 827069 | |
| AT4G15370 | Baruol synthase [Source:UniProtKB/Swiss-Prot;Acc:O23390] | BARS1 | 827203 |
| AT4G15760 | monooxygenase 1 [Source:TAIR;Acc:AT4G15760] | MO1 | 827255 |
| AT4G16370 | oligopeptide transporter [Source:TAIR;Acc:AT4G16370] | ATOPT3 | NA |
| AT4G18510 | CLE2 [Source:UniProtKB/TrEMBL;Acc:A0A178UVM8] | CLE2 | 827583 |
| AT4G19720 | Glycosyl hydrolase family protein with chitinase insertion domain [Source:TAIR;Acc:AT4G19720] | 827716 | |
| AT4G21680 | Protein NRT1/ PTR FAMILY 7.2 [Source:UniProtKB/Swiss-Prot;Acc:Q8GXN2] | NPF7.2 | 828255 |
| AT4G22460 | Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q9SUX3] | 828341 | |
| AT4G22640 | Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein [Source:UniProtKB/TrEMBL;Acc:O49645] | 828360 | |
| AT4G23190 | Cysteine-rich receptor-like protein kinase 11 [Source:UniProtKB/Swiss-Prot;Acc:Q9ZP16] | CRK11 | 828418 |
| AT4G23550 | WRKY29 [Source:UniProtKB/TrEMBL;Acc:A0A178V2E9] | WRKY29 | 828455 |
| AT4G23700 | Cation/H(+) antiporter 17 [Source:UniProtKB/Swiss-Prot;Acc:Q9SUQ7] | CHX17 | 828470 |
| AT4G25090 | Putative respiratory burst oxidase homolog protein G [Source:UniProtKB/Swiss-Prot;Acc:Q9SW17] | RBOHG | 828612 |
| AT4G25100 | Superoxide dismutase [Fe] 1, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:P21276] | FSD1 | 828613 |
| AT4G25820 | Xyloglucan endotransglucosylase/hydrolase [Source:UniProtKB/TrEMBL;Acc:A0A178UTG4] | XTH14 | 828687 |
| AT4G26050 | Plant intracellular Ras-group-related LRR protein 8 [Source:UniProtKB/Swiss-Prot;Acc:Q8RWE5] | PIRL8 | 828711 |
| AT4G30110 | Cadmium/zinc-transporting ATPase HMA2 [Source:UniProtKB/Swiss-Prot;Acc:Q9SZW4] | HMA2 | 829134 |
| AT4G31330 | Uncharacterized protein At4g31330 [Source:UniProtKB/TrEMBL;Acc:Q9C5C1] | 829260 | |
| AT4G33050 | calmodulin-binding family protein [Source:TAIR;Acc:AT4G33050] | EDA39 | 829442 |
| AT4G33880 | Transcription factor bHLH85 [Source:UniProtKB/Swiss-Prot;Acc:Q84WK0] | BHLH85 | 829531 |
| AT4G34135 | UDP-glucosyl transferase 73B2 [Source:UniProtKB/Swiss-Prot;Acc:Q94C57] | UGT73B2 | 829560 |
| AT4G37060 | PATATIN-like protein 5 [Source:TAIR;Acc:AT4G37060] | PLP5 | 829860 |
| AT4G37220 | Cold-regulated 413 plasma membrane protein 4 [Source:UniProtKB/Swiss-Prot;Acc:O23164] | 829876 | |
| AT4G37390 | Auxin-responsive GH3 family protein [Source:TAIR;Acc:AT4G37390] | YDK1 | NA |
| AT4G38970 | Fructose-bisphosphate aldolase [Source:UniProtKB/TrEMBL;Acc:A0A178UW98] | FBA2 | 830052 |
| AT4G39950 | cytochrome P450, family 79, subfamily B, polypeptide 2 [Source:TAIR;Acc:AT4G39950] | CYP79B2 | 830154 |
| AT5G01550 | lectin receptor kinase a4.1 [Source:TAIR;Acc:AT5G01550] | LECRKA4.2 | 831700 |
| AT5G02230 | Haloacid dehalogenase-like hydrolase (HAD) superfamily protein [Source:TAIR;Acc:AT5G02230] | 831784 | |
| AT5G02490 | Probable mediator of RNA polymerase II transcription subunit 37c [Source:UniProtKB/Swiss-Prot;Acc:P22954] | MED37D | 831856 |
| AT5G02780 | Glutathione S-transferase L1 [Source:UniProtKB/Swiss-Prot;Acc:Q6NLB0] | GSTL1 | 831800 |
| AT5G03545 | At5g03545 [Source:UniProtKB/TrEMBL;Acc:Q9LZD2] | AT4 | 831795 |
| AT5G04150 | basic helix-loop-helix (bHLH) DNA-binding superfamily protein [Source:TAIR;Acc:AT5G04150] | BHLH101 | 830293 |
| AT5G07760 | formin homology 2 domain-containing protein / FH2 domain-containing protein [Source:TAIR;Acc:AT5G07760] | 830669 | |
| AT5G09978 | Elicitor peptide 7 [Source:UniProtKB/Swiss-Prot;Acc:P0C1T5] | PEP7 | 5008207 |
| AT5G11650 | Alpha/beta-Hydrolases superfamily protein [Source:UniProtKB/TrEMBL;Acc:Q9LYG5] | 831037 | |
| AT5G11920 | Beta-fructofuranosidase, insoluble isoenzyme CWINV6 [Source:UniProtKB/Swiss-Prot;Acc:Q8W4S6] | CWINV6 | 831065 |
| AT5G12340 | DUF4228 domain protein [Source:UniProtKB/TrEMBL;Acc:Q1PDX4] | 831109 | |
| AT5G13190 | CONTAINS InterPro DOMAIN/s: LPS-induced tumor necrosis factor alpha factor (InterPro:IPR006629); Ha. [Source:TAIR;Acc:AT5G13190] | 831158 | |
| AT5G14730 | At5g14730 [Source:UniProtKB/TrEMBL;Acc:Q9LER3] | 831325 | |
| AT5G17820 | Peroxidase superfamily protein [Source:TAIR;Acc:AT5G17820] | 831650 | |
| AT5G19240 | Uncharacterized GPI-anchored protein At5g19240 [Source:UniProtKB/Swiss-Prot;Acc:Q84VZ5] | 832044 | |
| AT5G22555 | unknown protein; Ha. [Source:TAIR;Acc:AT5G22555] | 832318 | |
| AT5G22890 | Protein SENSITIVE TO PROTON RHIZOTOXICITY 2 [Source:UniProtKB/Swiss-Prot;Acc:Q0WT24] | STOP2 | 832353 |
| AT5G24240 | Phosphatidylinositol 4-kinase gamma 3 [Source:UniProtKB/Swiss-Prot;Acc:Q9FNF8] | PI4KG3 | 832491 |
| AT5G24530 | Protein DOWNY MILDEW RESISTANCE 6 [Source:UniProtKB/Swiss-Prot;Acc:Q9FLV0] | DMR6 | 832524 |
| AT5G24660 | Protein RESPONSE TO LOW SULFUR 2 [Source:UniProtKB/Swiss-Prot;Acc:Q9FIR9] | LSU2 | 832538 |
| AT5G25250 | Flotillin-like protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q501E6] | FLOT1 | 832596 |
| AT5G26690 | Heavy metal-associated isoprenylated plant protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q8GWS3] | HIPP02 | 832720 |
| AT5G27420 | E3 ubiquitin-protein ligase ATL31 [Source:UniProtKB/Swiss-Prot;Acc:Q8LGA5] | ATL31 | 832801 |
| AT5G35580 | Protein kinase superfamily protein [Source:TAIR;Acc:AT5G35580] | 833523 | |
| AT5G37485 | other RNA [Source:TAIR;Acc:AT5G37485] | NA | |
| AT5G37990 | Probable S-adenosylmethionine-dependent methyltransferase At5g37990 [Source:UniProtKB/Swiss-Prot;Acc:Q9FKC8] | 833778 | |
| AT5G38820 | 833873 | ||
| AT5G38910 | Putative germin-like protein subfamily 1 member 9 [Source:UniProtKB/Swiss-Prot;Acc:Q9FMB0] | 833883 | |
| AT5G38930 | Germin-like protein subfamily 1 member 10 [Source:UniProtKB/Swiss-Prot;Acc:Q9FMA9] | 833885 | |
| AT5G39460 | Putative F-box protein At5g39460 [Source:UniProtKB/Swiss-Prot;Acc:Q9FLZ1] | 833942 | |
| AT5G39580 | Peroxidase 62 [Source:UniProtKB/Swiss-Prot;Acc:Q9FKA4] | PER62 | 833954 |
| AT5G39630 | Vesicle transport v-SNARE family protein [Source:UniProtKB/TrEMBL;Acc:Q1PDQ2] | 833959 | |
| AT5G41740 | Disease resistance protein (TIR-NBS-LRR class) family [Source:UniProtKB/TrEMBL;Acc:F4JYI4] | 834177 | |
| AT5G41750 | Disease resistance protein (TIR-NBS-LRR class) family [Source:UniProtKB/TrEMBL;Acc:Q9LSX5] | 834178 | |
| AT5G42830 | HXXXD-type acyl-transferase family protein [Source:UniProtKB/TrEMBL;Acc:Q9FMN6] | 834294 | |
| AT5G43520 | Cysteine/Histidine-rich C1 domain family protein [Source:UniProtKB/TrEMBL;Acc:Q9FIY8] | 834372 | |
| AT5G44020 | HAD superfamily, subfamily IIIB acid phosphatase [Source:UniProtKB/TrEMBL;Acc:Q9FNC4] | 834425 | |
| AT5G44380 | FAD-binding Berberine family protein [Source:TAIR;Acc:AT5G44380] | 834464 | |
| AT5G45090 | Uncharacterized protein PHLOEM PROTEIN 2-LIKE A7 [Source:UniProtKB/Swiss-Prot;Acc:Q9FHE5] | PP2A7 | 834541 |
| AT5G45110 | NPR3 [Source:UniProtKB/TrEMBL;Acc:A0A178UGU4] | NPR3 | 834545 |
| AT5G45220 | Disease resistance protein (TIR-NBS-LRR class) family [Source:UniProtKB/TrEMBL;Acc:Q9FKE3] | 834558 | |
| AT5G45380 | DUR3 [Source:UniProtKB/TrEMBL;Acc:A0A178UG75] | DUR3 | 834574 |
| AT5G45490 | Probable disease resistance protein At5g45490 [Source:UniProtKB/Swiss-Prot;Acc:Q9FHI7] | 834585 | |
| AT5G47240 | nudix hydrolase homolog 8 [Source:TAIR;Acc:AT5G47240] | atnudt8 | 834771 |
| AT5G47980 | BAHD acyltransferase At5g47980 [Source:UniProtKB/Swiss-Prot;Acc:Q9FI40] | BAHD1 | 834849 |
| AT5G48430 | At5g48430 [Source:UniProtKB/TrEMBL;Acc:Q9LV70] | 834898 | |
| AT5G48850 | ATSDI1 [Source:UniProtKB/TrEMBL;Acc:A0A178UKA2] | SDI1 | 834943 |
| AT5G50760 | At5g50760 [Source:UniProtKB/TrEMBL;Acc:Q9LUE5] | 835148 | |
| AT5G52350 | Exocyst subunit Exo70 family protein [Source:UniProtKB/TrEMBL;Acc:F4KG58] | ATEXO70A3 | 835311 |
| AT5G53250 | ATAGP22 [Source:UniProtKB/TrEMBL;Acc:A0A178UC75] | AGP22 | 835406 |
| AT5G53450 | Probable plastid-lipid-associated protein 14, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:Q9LV04] | PAP14 | 835426 |
| AT5G54710 | Ankyrin repeat family protein [Source:TAIR;Acc:AT5G54710] | 835560 | |
| AT5G57220 | Cytochrome P450 81F2 [Source:UniProtKB/Swiss-Prot;Acc:Q9LVD6] | CYP81F2 | 835828 |
| AT5G60660 | PIP2F [Source:UniProtKB/TrEMBL;Acc:A0A178UG45] | PIP2-4 | 836187 |
| AT5G60780 | High affinity nitrate transporter 2.3 [Source:UniProtKB/Swiss-Prot;Acc:Q9FJH7] | NRT2.3 | 836199 |
| AT5G60900 | receptor-like protein kinase 1 [Source:TAIR;Acc:AT5G60900] | RLK1 | NA |
| AT5G61820 | Stress up-regulated Nod 19 protein [Source:UniProtKB/TrEMBL;Acc:Q8VZ21] | 836304 | |
| AT5G64100 | Peroxidase [Source:UniProtKB/TrEMBL;Acc:A0A178U798] | PER69 | 836531 |
| AT5G67340 | U-box domain-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5XEZ8] | PUB2 | 836869 |
sharedBy4 <- unique(unlist(subset(partitions, partitions$shared == 3)$..values..))
a <- OntologyProfileAt(sharedBy4)d <- data.frame(matrix(ncol = 4, nrow = 2))
colnames(d) <- names(g)
row.names(d) <- c("up", "down")
for (comp in names(g)) {
d["up", comp] <- sum(g[[comp]]$upreg == 1)
d["down", comp] <- sum(g[[comp]]$upreg == 0)
}
res <- melt(d)
res$reg = rep(c("up", "down"), 4)
ggplot(res, aes(fill = reg, y = value, x = variable)) + geom_bar(position = "stack",
stat = "identity") + ggtitle("Nitrate effet on gene regulation") + xlab("") +
ylab("Number of differentially expressed genes") + coord_flip()